SIMULATION AND MODELING OF MICROORGANISMS IN BIOFILM
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Date
2021-05
Authors
Bissembayeva, Gulzhahan
Journal Title
Journal ISSN
Volume Title
Publisher
Nazarbayev University School of Engineering and Digital Sciences
Abstract
Biofilms are microstructured microbial communities that form at interfacies. In
biofilms, microbial cells are encased in a matrix comprising polysaccharides, proteins, and
extracelluar DNA. In the environment, biofilms contribute to biogeochemical cycles and
pollutant degradation. However, biofilms are also responsible for more than 60% of infections
and 80% of chronic infections [1, 2]. The phenotype of microorganisms in the biofilm is
different compared to those in the planktonic state. Bacteria in biofilms have increased
resistance to antibiotics, faster mutation accumulation rate, and higher virulence [3-10]. Biofilm
are heterogenous and dynamic systems, in which biomass self-organize in response to nutrient
availability, flow conditions, etc. While numerous techniques exist for biofilm growth and
analysis, biofilm modeling allows simulating a broad range of growth conditions and provide
preliminary information that reduce the number of experiments. Among others, agent-based
models (ABM) have been used to simulate biofilm formation and growth. In these models, cells
are described as individual automata that follow a simple set of rules (rules of life) to interact
between each other and with the surrounding environment. While ABMs can be coded in any
language, they are easy to implement in NetLogo, a simplified multi-agent programmable
environment for modelling designed specifically for ABMs. In this thesis, the bacterial
attachment, growth and biofilm propagation were modeled using the NetLogo. The model was
run using parameters extracted from previous literature. This work provides a simple
framework to test biofilm formation, propagation and dispersal in capillaries and other simple
biomedical devices.
Description
Keywords
DNA, biofilm, pseudomonas aeruginosa, PA, Research Subject Categories::TECHNOLOGY, agent-based model, ABM, Type of access: Embargo
Citation
Bissembayeva, G. (2021). Simulation and Modeling of Microorganisms in Biofilm (Unpublished master's thesis). Nazarbayev University, Nur-Sultan, Kazakhstan